User:Karl Oberholser

Karl Oberholser
Professor Emeritus, Chemistry and Biochemistry Department, Messiah College, Grantham, PA, USA  oberhols@messiah.edu  I used HyperChem in my first venture in biomolecular visualization and computation. I eventually made some tutorials in which information was passed between HyperChem and Toolbook. When I became aware of Chime, I focused most of my work on protein structure and function and used Protein Explorer (PE) and Presentations in PE (PiPEs) as they became available. When MolSlides became a feature of PE, I developed an assignment for biochemistry students to make MolSlides of a protein of their choice. In the early years of this work I received a variety of internal grants from Messiah College, and in more recent years I have been receiving release time from teaching. Realizing that Chime was on its death bed I got serious about learning Jmol during the Summer '07, and during my Fall '07 sabbatical I ported most of the PiPEs to Jmol and converted the last of the HyperChem scripts to Jmol scripts. For most of this work I used &alpha; and &beta; versions of Jmol Tutorial-Authoring Template being made by Eric Martz. My first exposure to Proteopedia was mentoring Emily Forschler as she developed Photosystem II.

Proteopedia Pages
Topics related to proteins Specific proteins Topics related to Nucleic acids
 * Psi_and_Phi_Angles
 * Ramachandran_Plots
 * Fibroins
 * Alpha-helical coiled-coil
 * Globular Proteins
 * Oxymyoglobin
 * Archaeal_Histones - Illustrates the structural features of two histones and the dimer of one of them.
 * Collagen - Illustrates the structure of a collagen segment as well as the structure of a mutated tropocollagen.
 * Complex III of Electron Transport Chain - After illustration of the structures and relative positions of the active peptides, the reactions of the Q cycle are illustrated and explained.
 * User:Karl_Oberholser/PPDK_large - Large frame of a movie of the mechanism of pyruvate phosphate dikinase. The original page with a smaller movie frame and a description of the mechanism is here.
 * User:Karl_Oberholser/Phosphoenolpyruvate:Sugar_Phosphotransferase - Large frame of a movie of the mechanism of Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System. The original page with a smaller movie frame and a description of the system and mechanism is here.
 * Syn_and_anti_nucleosides - Illustrates the structural difference between the syn and anti configurations of nucleosides and the steric hindrance that is present in the syn configuration of pyrimidine nucleosides.
 * User:Karl Oberholser/Sandbox 1 - sandbox for my development work

Other structures and tutorials available in Jmol

 * Klotho Biochemicals in Jmol - A searchable list of common biochemicals whose structures can be displayed conveniently in Jmol.
 * Acetylcholinesterase
 * Carbohydrates - Series of tutorials that focus on aspects of the 3D structure of mono-, di-, and polysaccharides that are not easily illustrated with 2D figures in text books.
 * Biomodel-3 - 3D structures of carbohydrates, lipids, amino acids, nucleic acids.

Helpful Pages

 * Help:Editing
 * Help:Color_Keys
 * Small Molecules
 * Proteopedia:Wishlist
 * Proteopedia:Problems
 * What's_new
 * Template:Button_Toggle_Animation
 * Teaching_Strategies_Using_Proteopedia
 * Files uploaded by Karl Obeerholser
 * Jena3D Viewer